The power of Xmipp

Xmipp is a key software suite in the image processing workflow for cryo-electron microscopy (cryo-EM) single-particle analysis. Its modular protocols and deep integration with Scipion enable users to handle the complexity of cryo-EM data and achieve high-resolution 3D reconstructions.

This page highlights the relevance of Xmipp through two concrete examples: ClpC1P1P2 and HER2-TZB. In both cases, Xmipp protocols played a critical role in various stages of data processing, from preprocessing and particle selection to final 3D refinement and validation.

Example: HER2-TZB project

Project Summary

Protein: [To be completed]
Final Resolution: [To be completed]
Number of Movies: [To be completed]
EMDB ID: [To be completed]
Resolution Method: [To be completed]
Xmipp Version: [To be completed]

Protocols Used

CTF Correction: - XmippProtCTFCorrectWiener2D
Volume Processing and Refinement: - XmippProtAlignVolumeParticles - XmippProtReconstructFourier - XmippProtPreprocessVolumes - XmippProtFilterVolumes - XmippProtMaskVolumes - XmippProtMonoRes - XmippProtStructureMap - XmippProtSubtractProjection
Particle Handling: - XmippProtCropResizeParticles
3D Visualization and Validation: - XmippProtCompareAngles - XmippProtCompareReprojections - XmippProtConsensusClasses - XmippProtCreateGallery - XmippProtCreateMask3D - XmippProtFSO
Postprocessing: - emhancer
Model Integration: - XmippProtConvertPdb

Conclusion

The projects above exemplify how Xmipp provides a comprehensive toolbox that supports end-to-end cryo-EM workflows. From CTF correction to final volume polishing and validation, Xmipp’s protocols are critical in producing reliable, reproducible, and high-quality structural data.

Future developments in Xmipp continue to incorporate state-of-the-art techniques such as deep learning, automation, and hybrid modeling to push the boundaries of cryo-EM analysis.